Direction on managing multiple datasets

Are the excel spreadsheets that each one is completing the same?

If so you could possibly use the append feature in the Power Query Editor to combine each of the datasets into one.  You would want a column either added to the excel spreadsheets that designates which facility the data was coming from or add a custom column on each of those datasets in power query prior to the append.

Then you can have one report.

Grant the users access to the report and then in security you could limit each of them to their respective facility using row level security.

I havent setup the online scheduled refresh from the one drive folder but I think that is pretty common.

The new dataflows could possibly play a role here as well if you wanted reuse that dataset with multiple reports.